S6 bolt-on or glued neck?

Yes that's true to check relief you need the guitar tuned to pitch you use could be a half step or even a hole step flat or 440.
I only brought this up because if the rod has not been touched in years or never touched at all on a two way rod it could be difficult to turn and you can't get access to lube the threads. There may also be glue interfering. Some rods have a heat shrink covering the rod some don't.

I just stay on the side of caution, if you do break the rod or more likely the welded on adjustment head and I've read it's happened even on the rods Stewmac offers. It's fine to loosen a rod under string tension as long as you are sure it turns free before hand. If for any reason it does break then it's a lot of work to replace it, as you know.

I have a 2009 Epiphone AJ-100 I got on sale at Sam Ash not much more than $70. It has a two way rod adjustment at the peghead. It was never adjusted until I did it early this year . I used the long end of the L shaped hex key in the rod and used the short end to see how it felt backing off and it was stuck. I just worked it each direction a bit until it would turn then backed it off CCW until is stopped then turned it CW until it felt free.

I only bring this up since the original post brought up the issue he could not get less than .012" relief and stated the rod would hit it's stop. You should be able to adjust a 2 two rod to set the neck to no relief and even into a back bow if the rod is working as designed. If this can't be done then perhaps the rod was not threaded far enough or there may be glue on the threads which would not allow enough travel.

On all the electrics I've built I always used and prefer one way rods since you can work the nut off and lightly lube the threads and if you build the neck correct dead level the strings should pull in relief. This may not always happen with really light gauge strings and this is mainly why two way rods were designed. I used the type with the aluminum U channel on 4 strats I built and prefer to have a wood strip over the rod rather than have it bearing on the fingerboard as most do now. I did use one of Stewmac's dual action Hot Rod truss rods on the last strat I built and sold and they instruct you to place a dab of silicone at each end for rattles and route the slot so the rod brass ends are flush with the routes top. I routed a 1/16" deeper and added a wood filler strip. Before that on my first builds in 84 until 1990 I made my own single action out of 3/16" hardened steel rod which are set low in the neck with a wood filler strip. I used hex shaped 1" long threaded nuts from the hardware store and a thick hard washer, the type one used to connect 2 threaded rod together.